Prevalence, Molecular Detection, and In Vitro Elimination of Latent Viruses and Viroids in Pome Fruit Germplasm of Kazakhstan

Latent viral and viroid infections represent a major phytosanitary threat to pome fruit production because infected propagation material facilitates the long-term spread of pathogens in orchards. This study investigated the prevalence of viral and viroid pathogens in apple and pear orchards of southern and southeastern Kazakhstan and evaluated the efficiency of integrated in vitro sanitation approaches. A total of 34 samples collected from commercial orchards were analyzed using RT-qPCR. Apple stem pitting virus (ASPV) was the most prevalent pathogen detected across all surveyed regions, followed by Apple chlorotic leaf spot virus (ACLSV). Apple stem grooving virus (ASGV), Apple hammerhead viroid (AHVd), Apple mosaic virus (ApMV), and Apple rubbery wood virus 1 (ARWV-1) were detected at lower frequencies. Notably, ARWV-1 and AHVd were detected exclusively in the Almaty Region, representing their first molecular detection in Kazakhstan. Mixed infections were common, and visual symptoms did not consistently correlate with molecular detection results, emphasizing the importance of RT-qPCR for reliable phytosanitary diagnostics. Integrated sanitation methods combining thermotherapy, chemotherapy, cryotherapy, and meristem culture effectively eliminated viral and viroid infections from infected apple and pear genotypes. Ribavirin at 15 mg L−1 provided the optimal balance between antiviral activity and explant viability. Complete elimination of ACLSV, AHVd, ASPV, ASGV, ApMV, and ARWV-1 was achieved after combined treatment, while regenerated plants maintained stable micropropagation capacity. The obtained results demonstrate the necessity of routine molecular monitoring and support the development of virus-free certification systems for pome fruit crops in Kazakhstan.